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Leiva C, Pérez-Sorribes L, González-Delgado S, Ortiz S, Wangensteen OS, Pérez-Portela R. Exceptional population genomic homogeneity in the black brittle star Ophiocomina nigra (Ophiuroidea, Echinodermata) along the Atlantic-Mediterranean coast. Sci Rep 2023; 13:12349. [PMID: 37524805 PMCID: PMC10390532 DOI: 10.1038/s41598-023-39584-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/27/2023] [Indexed: 08/02/2023] Open
Abstract
The Atlantic-Mediterranean marine transition is characterised by strong oceanographic barriers and steep environmental gradients that generally result in connectivity breaks between populations from both basins and may lead to local adaptation. Here, we performed a population genomic study of the black brittle star, Ophiocomina nigra, covering most of its distribution range along the Atlantic-Mediterranean region. Interestingly, O. nigra is extremely variable in its coloration, with individuals ranging from black to yellow-orange, and different colour morphs inhabiting different depths and habitats. In this work, we used a fragment of the mitochondrial COI gene and 2,374 genome-wide ddRADseq-derived SNPs to explore: (a) whether the different colour morphs of O. nigra represent different evolutionary units; (b) the disruptive effects of major oceanographic fronts on its population structure; and (c) genomic signals of local adaptation to divergent environments. Our results revealed exceptional population homogeneity, barely affected by oceanographic fronts, with no signals of local adaptation nor genetic differentiation between colour morphs. This remarkable panmixia likely results from a long pelagic larval duration, a large effective population size and recent demographic expansions. Our study unveils an extraordinary phenotypic plasticity in O. nigra, opening further research questions on the ecological and molecular mechanisms underpinning coloration in Ophiuroidea.
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Affiliation(s)
- Carlos Leiva
- Departament de Biologia Evolutiva, Facultat de Biologia, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Av. Diagonal 643, 08028, Barcelona, Spain.
- University of Guam Marine Laboratory, 303 University Drive, Mangilao, GU, 96923, USA.
| | - Laia Pérez-Sorribes
- Departament de Biologia Evolutiva, Facultat de Biologia, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Av. Diagonal 643, 08028, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Sara González-Delgado
- Departamento de Biología Animal, Edafología y Geología, Facultad de Ciencias, Universidad de la Laguna, Canary Islands, Spain
| | - Sandra Ortiz
- Departament de Biologia Evolutiva, Facultat de Biologia, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Av. Diagonal 643, 08028, Barcelona, Spain
| | - Owen S Wangensteen
- Departament de Biologia Evolutiva, Facultat de Biologia, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Av. Diagonal 643, 08028, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Rocío Pérez-Portela
- Departament de Biologia Evolutiva, Facultat de Biologia, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Av. Diagonal 643, 08028, Barcelona, Spain.
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
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Not all is black and white: phylogeography and population genetics of the endemic blackbuck (Antilope cervicapra). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01479-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Riesgo A, Taboada S, Pérez-Portela R, Melis P, Xavier JR, Blasco G, López-Legentil S. Genetic diversity, connectivity and gene flow along the distribution of the emblematic Atlanto-Mediterranean sponge Petrosia ficiformis (Haplosclerida, Demospongiae). BMC Evol Biol 2019; 19:24. [PMID: 30651060 PMCID: PMC6335727 DOI: 10.1186/s12862-018-1343-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 12/28/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Knowledge about the distribution of the genetic variation of marine species is fundamental to address species conservation and management strategies, especially in scenarios with mass mortalities. In the Mediterranean Sea, Petrosia ficiformis is one of the species most affected by temperature-related diseases. Our study aimed to assess its genetic structure, connectivity, and bottleneck signatures to understand its evolutionary history and to provide information to help design conservation strategies of sessile marine invertebrates. RESULTS We genotyped 280 individuals from 19 locations across the entire distribution range of P. ficiformis in the Atlanto-Mediterranean region at 10 microsatellite loci. High levels of inbreeding were detected in most locations (especially in the Macaronesia and the Western Mediterranean) and bottleneck signatures were only detected in Mediterranean populations, although not coinciding entirely with those with reported die-offs. We detected strong significant population differentiation, with the Atlantic populations being the most genetically isolated, and show that six clusters explained the genetic structure along the distribution range of this sponge. Although we detected a pattern of isolation by distance in P. ficiformis when all locations were analyzed together, stratified Mantel tests revealed that other factors could be playing a more prominent role than isolation by distance. Indeed, we detected a strong effect of oceanographic barriers impeding the gene flow among certain areas, the strongest one being the Almeria-Oran front, hampering gene flow between the Atlantic Ocean and the Mediterranean Sea. Finally, migration and genetic diversity distribution analyses suggest a Mediterranean origin for the species. CONCLUSIONS In our study Petrosia ficiformis showed extreme levels of inbreeding and population differentiation, which could all be linked to the poor swimming abilities of the larva. However, the observed moderate migration patterns are highly difficult to reconcile with such poor larval dispersal, and suggest that, although unlikely, dispersal may also be achieved in the gamete phase. Overall, because of the high genetic diversity in the Eastern Mediterranean and frequent mass mortalities in the Western Mediterranean, we suggest that conservation efforts should be carried out specifically in those areas of the Mediterranean to safeguard the genetic diversity of the species.
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Affiliation(s)
- Ana Riesgo
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Sergi Taboada
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Department of Biology (Zoology), Autonomous University of Madrid, Faculty of Sciences, Cantoblanco, 28049 Madrid, Spain
| | - Rocío Pérez-Portela
- Department of Geology and Biology, Physics and Inorganic Chemistry, King Juan Carlos I University, C/ Tulipán s.n, 28933 Móstoles, Madrid Spain
| | - Paolo Melis
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - Joana R. Xavier
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, 4450-208 Matosinhos, Portugal
- Department of Biology, KG Jebsen Centre for Deep-Sea Research, University of Bergen, Thormøhlensgate 53A, 5006 Bergen, Norway
| | - Gema Blasco
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409 USA
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Spatio-temporal patterns of genetic variation in Arbacia lixula, a thermophilous sea urchin in expansion in the Mediterranean. Heredity (Edinb) 2018; 122:244-259. [PMID: 29904170 DOI: 10.1038/s41437-018-0098-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 01/06/2023] Open
Abstract
The genetic structure of 13 populations of the amphiatlantic sea urchin Arbacia lixula, as well as temporal genetic changes in three of these localities, were assessed using ten hypervariable microsatellite loci. This thermophilous sea urchin is an important engineer species triggering the formation of barren grounds through its grazing activity. Its abundance seems to be increasing in most parts of the Mediterranean, probably favoured by warming conditions. Significant genetic differentiation was found both spatially and temporally. The main break corresponded to the separation of western Atlantic populations from those in eastern Atlantic and the Mediterranean Sea. A less marked, but significant differentiation was also found between Macaronesia (eastern Atlantic) and the Mediterranean. In the latter area, a signal of differentiation between the transitional area (Alboran Sea) and the rest of the Mediterranean was detected. However, no genetic structure is found within the Mediterranean (excluding Alboran) across the Siculo-Tunisian Strait, resulting from either enough gene flow to homogenize distance areas or/and a recent evolutionary history marked by demographic expansion in this basin. Genetic temporal variation at the Alboran Sea is as important as spatial variation, suggesting that temporal changes in hydrological features can affect the genetic composition of the populations. A picture of genetic homogeneity in the Mediterranean emerges, implying that the potential expansion of this keystone species will not be limited by intraspecific genetic features and/or potential impact of postulated barriers to gene flow in the region.
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Costantini F, Ferrario F, Abbiati M. Chasing genetic structure in coralligenous reef invertebrates: patterns, criticalities and conservation issues. Sci Rep 2018; 8:5844. [PMID: 29643422 PMCID: PMC5895814 DOI: 10.1038/s41598-018-24247-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 03/27/2018] [Indexed: 12/02/2022] Open
Abstract
Conservation of coastal habitats is a global issue, yet biogenic reefs in temperate regions have received very little attention. They have a broad geographic distribution and are a key habitat in marine ecosystems impacted by human activities. In the Mediterranean Sea coralligenous reefs are biodiversity hot spots and are classified as sensitive habitats deserving conservation. Genetic diversity and structure influence demographic, ecological and evolutionary processes in populations and play a crucial role in conservation strategies. Nevertheless, a comprehensive view of population genetic structure of coralligenous species is lacking. Here, we reviewed the literature on the genetic structure of sessile and sedentary invertebrates of the Mediterranean coralligenous reefs. Linear regression models and meta-analytic approaches are used to assess the contributions of genetic markers, phylum, pelagic larval duration (PLD) and geographical distance to the population genetic structure. Our quantitative approach highlight that 1) most species show a significant genetic structure, 2) structuring differs between phyla, and 3) PLD does not appear to be a major driver of the structuring. We discuss the implication of these finding for the management and conservation, suggesting research areas that deserve attention, and providing recommendations for broad assessment and monitoring of genetic diversity in biogenic reefs species.
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Affiliation(s)
- Federica Costantini
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, UOS Ravenna, Ravenna, Italy.
- Centro Interdipartimentale di Ricerca per le Scienze Ambientali, Università di Bologna, Via S. Alberto 163, I - 48123, Ravenna, Italy.
- CoNISMa, Piazzale Flaminio 9, 00197, Roma, Italy.
| | | | - Marco Abbiati
- Centro Interdipartimentale di Ricerca per le Scienze Ambientali, Università di Bologna, Via S. Alberto 163, I - 48123, Ravenna, Italy
- CoNISMa, Piazzale Flaminio 9, 00197, Roma, Italy
- Dipartimento di Beni Culturali, Via degli Ariani, 1, 48121, Ravenna, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine, ISMAR, Via P. Gobetti 101, 40129, Bologna, Italy
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Garcia-Cisneros A, Palacín C, Ventura CRR, Feital B, Paiva PC, Pérez-Portela R. Intraspecific genetic structure, divergence and high rates of clonality in an amphi-Atlantic starfish. Mol Ecol 2018; 27:752-772. [PMID: 29218784 DOI: 10.1111/mec.14454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/28/2017] [Accepted: 11/08/2017] [Indexed: 12/14/2022]
Abstract
Intraspecific genetic diversity and divergence have a large influence on the adaption and evolutionary potential of species. The widely distributed starfish, Coscinasterias tenuispina, combines sexual reproduction with asexual reproduction via fission. Here we analyse the phylogeography of this starfish to reveal historical and contemporary processes driving its intraspecific genetic divergence. We further consider whether asexual reproduction is the most important method of propagation throughout the distribution range of this species. Our study included 326 individuals from 16 populations, covering most of the species' distribution range. A total of 12 nuclear microsatellite loci and sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analysed. COI and microsatellites were clustered in two isolated lineages: one found along the southwestern Atlantic and the other along the northeastern Atlantic and Mediterranean Sea. This suggests the existence of two different evolutionary units. Marine barriers along the European coast would be responsible for population clustering: the Almeria-Oran Front that limits the entrance of migrants from the Atlantic to the Mediterranean, and the Siculo-Tunisian strait that divides the two Mediterranean basins. The presence of identical genotypes was detected in all populations, although two monoclonal populations were found in two sites where annual mean temperatures and minimum values were the lowest. Our results based on microsatellite loci showed that intrapopulation genetic diversity was significantly affected by clonality whereas it had lower effect for the global phylogeography of the species, although still some impact on populations' genetic divergence could be observed between some populations.
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Affiliation(s)
- Alex Garcia-Cisneros
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Research Institute of Biodiversity (IRBIO), Barcelona, Spain.,Center for Advanced Studies of Blanes (CEAB-CSIC), Accès a la Cala Sant Francesc, Girona, Spain
| | - Creu Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Research Institute of Biodiversity (IRBIO), Barcelona, Spain
| | - Carlos Renato Rezende Ventura
- Invertebrate Department, National Museum, Federal University of Rio de Janeiro, Quinta da Boa Vista, Rio de Janeiro, Brazil
| | - Barbara Feital
- Invertebrate Department, National Museum, Federal University of Rio de Janeiro, Quinta da Boa Vista, Rio de Janeiro, Brazil.,Department of Zoology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo Cesar Paiva
- Department of Zoology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rocío Pérez-Portela
- Center for Advanced Studies of Blanes (CEAB-CSIC), Accès a la Cala Sant Francesc, Girona, Spain
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Sanna D, Lai T, Cossu P, Scarpa F, Dedola GL, Cristo B, Francalacci P, Curini-Galletti M, Mura L, Fois N, Maltagliati F, Casu M. Cytochrome c oxidase subunit I variability in Ruditapes decussatus (Veneridae) from the western Mediterranean. EUROPEAN ZOOLOGICAL JOURNAL 2017. [DOI: 10.1080/24750263.2017.1395914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- D. Sanna
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - T. Lai
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - P. Cossu
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - F. Scarpa
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - G. L. Dedola
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - B. Cristo
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - P. Francalacci
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - M. Curini-Galletti
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - L. Mura
- Dipartimento per la Ricerca nelle Produzioni Animali, Agris Sardegna, Agenzia per la Ricerca in Agricoltura , Olmedo (SS), Italy
| | - N. Fois
- Dipartimento per la Ricerca nelle Produzioni Animali, Agris Sardegna, Agenzia per la Ricerca in Agricoltura , Olmedo (SS), Italy
| | - F. Maltagliati
- Dipartimento di Biologia, Università di Pisa , Pisa (PI), Italy
| | - M. Casu
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
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Reduced genetic diversity and alteration of gene flow in a fiddler crab due to mangrove degradation. PLoS One 2017; 12:e0182987. [PMID: 28837577 PMCID: PMC5570428 DOI: 10.1371/journal.pone.0182987] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/27/2017] [Indexed: 11/19/2022] Open
Abstract
The fiddler crab Austruca occidentalis is a dominant species in mangrove forests along the East African coast. It enhances soil aeration and, through its engineering activities, makes otherwise-inaccessible food available for other marine organisms. Despite its importance, the habitat of A. occidentalis is threatened by human activities. Clearing the mangroves for salt farming and selective logging of mangroves trees continue to jeopardise mangrove ecosystems in the Western Indian Ocean. This study aims to use partial mitochondrial COI gene sequences and nuclear microsatellites to determine whether salt farming activities in mangroves have a negative impact on the genetic diversity and gene flow of A. occidentalis collected along the Tanzania coast. The level of genetic diversity for both mitochondrial DNA and nuclear microsatellites are relatively lower in samples from salt ponds compared to natural mangrove sites. Analysis of molecular variance (AMOVA) among all populations showed low but significant differentiation (COI: Fst = 0.022, P < 0.05; microsatellites: Fst = 0.022, P < 0.001). A hierarchical AMOVA indicates lower but significant genetic differentiation among populations from salt ponds and natural mangroves sites (COI: Fct = 0.033, P < 0.05; microsatellites: Fct = 0.018, P = < 0.01). These results indicate that salt farming has a significant negative impact on the genetic diversity of A. occidentalis. Since higher genetic diversity contributes to a stable population, restoring the cleared habitats might be the most effective measures for the conservation of genetic diversity and hence adaptive potential to environmental change in this species.
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Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries. Sci Rep 2016; 6:39152. [PMID: 27991535 PMCID: PMC5171699 DOI: 10.1038/srep39152] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/18/2016] [Indexed: 01/25/2023] Open
Abstract
In a resource management perspective, the understanding of the relative influence of the physical factors on species connectivity remains a major challenge and is also of great ecological and conservation biology interest. Despite the overfishing threat on the wedge clam Donax trunculus in Europe, relatively little information is known about its population genetic structure and connectivity and their consequences on conservation policies. We employed 16 microsatellite loci to characterise the genetic diversity and population structure of D. trunculus. A total of 514 samples from seven different localities along the Atlantic-Mediterranean transition, from the Atlantic (Gulf of Cádiz) to the north-western Mediterranean were genotyped. The analysis of the population genetic structure displayed a clear distinction along the Atlantic-Mediterranean transition with different clusters in the Atlantic Ocean, the Alboran Sea and the northwestern Mediterranean. Consequently, we recommend that these three areas should be considered as different management units. We showed that all populations seem to be at high long-term risk of extinction with the exception of the protected Doñana National Park population which still seems to have evolutionary potential. Therefore, our results emphasized the necessity of protection of this economic resource and the validity of molecular tools to evaluate the population dynamics.
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